Prairie cordgrass (PCG) (<
italic>
Spartina pectinata<
/italic>
Link) has a high tolerance to soil salinity and waterlogging, therefore, it can thrive on marginal lands. Optimizing the nitrogen (N) input is crucial to achieving desirable biomass production of PCG without negatively impacting the environment. Thus, this study was based on the hypothesis that the use of legumes such as kura clover (<
italic>
Trifolium ambiguum<
/italic>
M. Bieb.) (KC) as an intercrop with PCG can provide extra N to the crop reducing the additional N fertilizer and mitigating soil surface greenhouse gas (GHG) emissions. Specific objective of the study was to assess the impact of PCG managed with different N rates [0 kg N ha<
sup>
-1<
/sup>
(PCG-0N), 75 kg N ha<
sup>
-1<
/sup>
(PCG-75N), 150 kg N ha<
sup>
-1<
/sup>
(PCG-150N), and 225 kg N ha<
sup>
-1<
/sup>
(PCG-255N)], and PCG intercropped with KC (PCG-KC) on GHG fluxes and biomass yield. The experimental site was established in 2010 in South Dakota under a marginally yielding cropland. The GHG fluxes were measured from 2014 through 2018 growing seasons using the static chamber. Net global warming potential (GWP) was calculated. Data showed that cumulative CH<
sub>
4<
/sub>
and CO<
sub>
2<
/sub>
fluxes were similar for all the treatments over the study period. However, the PCG-KC, PCG-0N, and PCG-75N recorded lower cumulative N<
sub>
2<
/sub>
O fluxes (384, 402, and 499 g N ha<
sup>
-1<
/sup>
, respectively) than the PCG-150N (644 g N ha<
sup>
-1<
/sup>
) and PCG-255N (697 g N ha<
sup>
-1<
/sup>
). The PCG-KC produced 85% and 39% higher yield than the PCG-0N in 2016 and 2017, respectively, and similar yield to the other treatments (PCG-75N, PCG-150N, and PCG-255N) in these years. Net GWP was 52% lower for the PCG-KC (112.38 kg CO<
sub>
2<
/sub>
-eq ha<
sup>
-1<
/sup>
) compared to the PCG-225N (227.78 kg CO<
sub>
2<
/sub>
-eq ha<
sup>
-1<
/sup>
), but similar to other treatments. Soil total N was 15%% and 13% higher under PCG-KC (3.7 g kg<
sup>
-1<
/sup>
) than that under PCG-0N (3.2 g kg<
sup>
-1<
/sup>
) and PCG-75N (3.3 g kg<
sup>
-1<
/sup>
), respectively. This study concludes that intercropping prairie cordgrass with kura clover can enhance biomass yield and reduce fertilizer-derived N<
sub>
2<
/sub>
O emissions and net global warming potential.